[ headers, abspos, relpos, chroms, copydata] = readData('T10.100cells.cn.txt');
[ transVectors ] = getTransitionVectors(copydata);
[ codes, startSites, endSites] = collectAllCombinedTraits(transVectors)

for maxGap=0:5
    [ blendCodes, blendStarts, blendStartWindows, blendEnds, blendEndWindows ] = blendCombinedTraits( codes, startSites, endSites, maxGap );
    [ traitMatrix ] = getTraitMatrix( transVectors, blendCodes, blendStarts, blendStartWindows, blendEnds, blendEndWindows );
    [ tree ] = generateTree( traitMatrix, headers );
    p = plot(tree,'Orientation','top');
    title(maxGap);
end